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PREMISE OF THE STUDY: We explored the phylogenetic utility of entire plastid DNA sequences in Daucus and compared the results with prior phylogenetic results using plastid and nuclear DNA sequences. METHODS: We used Illumina sequencing to obtain full plastid sequences of 37 accessions of 20 Daucus taxa and outgroups, analyzed the data with phylogenetic methods, and examined evidence for mitochondrial DNA transfer to the plastid (DcMP). KEY RESULTS: Our phylogenetic trees of the entire data set were highly resolved, with 100% bootstrap support for most of the external and many of the internal clades, except for the clade of D. carota and its most closely related species D. syrticus. Subsets of the data, including regions traditionally used as phylogenetically informative regions, provide various degrees of soft congruence with the entire data set. There are areas of hard incongruence, however, with phylogenies using nuclear data. We extended knowledge of a mitochondrial to plastid DNA insertion sequence previously named DcMP and identified the first instance in flowering plants of a sequence of potential nuclear genome origin inserted into the plastid genome. There is a relationship of inverted repeat junction classes and repeat DNA to phylogeny, but no such relationship with nonsynonymous mutations. CONCLUSIONS: Our data have allowed us to (1) produce a well‐resolved plastid phylogeny of Daucus, (2) evaluate subsets of the entire plastid data for phylogeny, (3) examine evidence for plastid and nuclear DNA phylogenetic incongruence, and (4) examine mitochondrial and nuclear DNA insertion into the plastid.

Plastids in Nicotiana tabacum are normally transmitted to the progeny by the maternal parent only. However, low-frequency paternal plastid transmission has been reported in crosses involving parents with an alien cytoplasm. Our objective was to determine whether paternal plastids are transmitted in crosses between parents with the normal cytoplasm. The transplastomic father lines carried a spectinomycin resistance (aadA) transgene incorporated in the plastid genome. The mother lines in the crosses were either (i) alloplasmic, with the Nicotiana undulata cytoplasm that confers cytoplasmic male sterility (CMS92) or (ii) normal, with the fertile N. tabacum cytoplasm. Here we report that plastids from the transplastomic father were transmitted in both cases at low (10⁻⁴-10⁻⁵) frequencies; therefore, rare paternal pollen transmission is not simply due to breakdown of normal controls caused by the alien cytoplasm. Furthermore, we have found that the entire plastid genome was transmitted by pollen rather than small plastid genome (ptDNA) fragments. Interestingly, the plants, which inherited paternal plastids, also carried paternal mitochondrial DNA, indicating cotransmission of plastids and mitochondria in the same pollen. The detection of rare paternal plastid transmission described here was facilitated by direct selection for the transplastomic spectinomycin resistance marker in tissue culture; therefore, recovery of rare paternal plastids in the germline is less likely to occur under field conditions.

We conducted a molecular phylogenetic study of the tribe Stipeae using nine plastid DNA sequences (trnK-matK, matK, trnH-psbA, trnL-F, rps3, ndhF, rpl32-trnL, rps16-trnK, rps16 intron), the nuclear ITS DNA regions, and micromorphological characters from the lemma surface. Our large original dataset includes 156 accessions representing 139 species of Stipeae representing all genera currently placed in the tribe. The maximum likelihood and Bayesian analyses of DNA sequences provide strong support for the monophyly of Stipeae; including, in phylogenetic order, Macrochloa as remote sister lineage to all other Stipeae, then a primary stepwise divergence of three deep lineages with a saw-like (SL) lemma epidermal pattern (a plesiomorphic state). The next split is between a lineage (SL1) which bifurcates into separate Eurasian and American clades, and a lineage of three parts; a small Patis (SL2) clade, as sister to Piptatherum s.str. (SL3), and the achnatheroid clade (AC). The AC exhibits a maize-like lemma epidermal pattern throughout. AC consists of a core clade of Austral-Eurasian distribution and a \"major American clade\" of North and South American distribution. The base chromosome number for Stipeae is somewhat ambiguous but based on our survey it seems most likely to be x = 11 or 12. Our phylogenetic hypothesis supports the recognition of the following genera and groups (listed by region): Eurasia—Achnatherum, \"Miliacea group\", \"Neotrinia\" (monotypic), Orthoraphium (monotypic), Patis (also 1 from North America), Piptatherum s.str., Psammochloa (monotypic), Ptilagrostis, Stipa, \"Timouria group\", and Trikeraia; Mediterranean—Ampelodesmos (monotypic), Celtica (monotypic), Macrochloa (monotypic), and \"Stipella-Inaequiglumes group\"; Australasia—Anemanthele (monotypic), and Austrostipa: North America (NA)—\"Eriocoma group\", Hesperostipa, Oryzopsis (monotypic), Piptatheropsis, \"Pseudoeriocoma group\", and \"Stillmania\" (monotypic); South America—Aciachne, Amelichloa (also NA), Anatherostipa (s.str.), Jarava (polyphyletic), Lorenzochloa, Nassella (also NA), Ortachne, Pappostipa (also NA), and Piptochaetium (also NA). Monophyly of Phaenospermateae including Duthieinae is demonstrated, and its inclusion within or treatment as sister to Stipeae is rejected.

The genus Dyckia (Bromeliaceae) comprises more than 150 terrestrial or epilithic species with a strongly xeromorphic habit. Most of its members belong to the azonal rock vegetation of Neotropical savannas and forests of Brazil and adjacent countries. Dyckia is relatively species-rich compared with its closest relatives Encholirium (27 species) and Deuterocohnia (17 species). Here, we present the first molecular phylogenetic analysis of Dyckia using DNA sequence data from six plastid loci (matK gene, rps16 intron, petD intron, rpl32-trnL, rps16-trnK and trnD-trnT) and a portion of the nuclear gene phyC. A total of 124 accessions were included, corresponding to 79 taxa from six genera. Phylogenetic trees were generated using parsimony, likelihood and Bayesian methods. DNA sequence variation among Dyckia species turned out to be extremely low, and phylogenies were poorly resolved. The monophyly of Dyckia is supported, whereas evidence is provided that Encholirium is paraphyletic. Based on a dated plastid DNA tree, Dyckia experienced a recent radiation starting around 2.9 million years ago. Four major clades could be identified that roughly correspond to the geographic origin of the samples. A parsimony network based on plastid DNA haplotypes shows a star-like pattern, indicating recent range expansions. Our data are compatible with a scenario where Dyckia and Encholirium diverged in northeastern Brazil, whereas one lineage of Dyckia dispersed to southern Brazil from where a rapid colonization of suitable habitats was initiated. We discuss our results in relation to species delimitation in Dyckia.

Aim: Many plants, especially at high latitudes, have both widespread and highly discontinuous geographical distributions. To increase understanding of how such patterns originate, we examine genetic patterns in the arctic-alpine plant Sibbaldia procumbens. We evaluate the contributions of réfugia and the role of long-distance dispersal in shaping the current range of this species. Location: Northern Hemisphere, especially North America. Methods: We sampled Sibbaldia from 176 localities, including 168 for S. procumbens. We analysed sequence variation in three plastid DNA non-coding regions (the atpl-atpH and trnL-trnY intergenic spacers and the trnL · intron), performed Bayesian phylogenetic analyses and statistical parsimony analyses on the combined sequences, and analysed the geographical patterns of haplotype distribution and genetic diversity using data from all populations. Results: Sibbaldia procumbens probably originated in the mountains of South and East Asia. We identified highly distinct clades in Europe and North America, which overlapped on oceanic islands of the North Atlantic indicating long-distance dispersal capability. The North American dade included two lineages, one in California and the other widely distributed across the continent and North Atlantic.Haplotype diversity in the latter lineage was markedly higher to the south, suggesting mid-late Pleistocene southward displacement of North American populations with subsequent migration northwards into previously glaciated regions. In Europe, disjunct geographical regions generally harboured distinct haplotypes. Main conclusions: Multiple Pleistocene réfugia for S. procumbens occurred in both North America and Europe. North American réfugia existed in California and in the southern Rocky Mountains, but in contrast with most widespread arctic—alpine species we found no evidence for a Beringian refugium. Cryptic réfugia may have existed within the Cordilleran Ice Sheet. Episodes of range expansion and contraction and long-distance dispersal have all contributed to the genetic structure and widespread but fragmented distribution of this species.

At the end of the 1920s, Vavilov organized several potato-collecting missions in South and Central America. Vavilov and his colleagues, Juzepczuk and Bukasov, participated in these expeditions and worked on gathered material, designated two centers of potato varietal riches and diversity—the Peru–Bolivia high-mountain center and the southern coast of Chile. The WIR Herbarium holds authentic specimens of many taxa described by Russian taxonomists. Here, a set of 20 plastid DNA-specific markers was applied for 49 authentic herbarium specimens of Solanum tuberosum L. from the WIR Herbarium to analyze the genetic diversity of the landrace population collected by Juzepczuk in 1928 in southern–central Chile. Two plastid DNA types, T and A, and two chlorotypes were identified in herbarium specimens, with a clear predominance (96%) of chlorotype cpT_III. In addition, we analyzed 46 living Chilean accessions from the VIR field potato gene bank that were collected after the appearance of Phytophthora infestans in Chile. These living accessions were differentiated into four chlorotypes. Finding a D-type cytoplasm in living Chilean accessions that possess two new chlorotypes indicates a replacement of native cultivars and introgression from the wild Mexican species S. demissum that was actively used in breeding as a source of race-specific resistance to late blight.

Premise of the study: To understand the origins of C₄ grasslands, we must have a better interpretation of plant traits via phylogenetic reconstruction. Muhlenbergiinae, the largest subtribe of C₄ grasses in Mexico and the southwestern United States (with 176 species), is taxonomically poorly understood. METHODS: We conducted a phylogenetic analysis of 47 genera and 174 species using six plastid regions (ndhA intron, ndhF, rps16-trnK, rps16 intron, rps3, and rpl32-trnL) and the nuclear ITS 1 and 2 (ribosomal internal transcribed spacer) regions to infer evolutionary relationships and revise the classification. Key results: In our analyses, Muhlenbergia (ca. 153 species) is paraphyletic, with nine genera (Aegopogon, Bealia, Blepharoneuron, Chaboissaea, Lycurus, Muhlenbergia, Pereilema, Redfieldia, Schaffnerella, and Schedonnardus) found nested within. We recognized the following five well-supported monophyletic lineages within MUHLENBERGIA: subg. Muhlenbergia, with species that have phosphoenolpyruvate carboxykinase-like leaf anatomy and long, scaly rhizomes; subg. Trichochloa with long-lived species that are relatively tall (up to 3 m); subg. Clomena with 3-nerved upper glumes; sect. Pseudosporobolus species with narrow panicles and plumbeous spikelets; and sect. Bealia species with lemmas with hairy margins and midveins. CONCLUSIONS: We propose expanding the circumscription of Muhlenbergia to include the other nine genera in this subtribe and make the following new combinations: Muhlenbergia subg. Bealia, M. diandra, M. geminiflora, M. paniculata, M. phleoides, M. subg. Pseudosporobolus (also lectotipified), M. solisii, M. tricholepis. We also propose several new names: M. ammophila, M. columbi, M. plumosa. Our phylograms suggest that Muhlenbergia originated in North America because the sister (Sohnsia filifolia and Scleropogoninae) is composed of predominantly North American species.

Phragmites australis (common reed) is a widespread perennial grass of wetland habitats, with cryptic native and introduced subspecies in North America. We determined the relative abundance of the subspecies and the distributions of plastid DNA haplotypes throughout British Columbia, Canada, at the northwestern distribution limit of common reed in North America. Of 203 specimens assigned to subspecies using molecular markers, we identified only 9 plants as the introduced ssp. australis ; all remaining samples were the native ssp. americanus . The two subspecies co-occurred at only one locality. We identified four native haplotypes (one widespread in British Columbia and three others more localized) and two introduced haplotypes. Using plants of known haplotype, we assessed the utility of different morphological traits and trait combinations for distinguishing native and introduced subspecies in this geographic region. No single morphological trait was diagnostic, but principal components analysis and identification indices based on combinations of traits consistently separated the native and introduced subspecies in our sample. Two- or three-trait combinations of ligule length, lemma length and stem anthocyanic coloration gave the best separation. These indices could reduce the need for confirmation of the introduced subspecies using molecular tools, facilitating efforts to monitor and control this invasive plant.

The pantropical orchid genus Polystachya is the subject of ongoing taxonomic work. We inferred phylogenetic relationships in the genus using 5.3 kb of plastid DNA, for 83 out of ca. 240 species and 12 out of 15 sections, as well as five outgroup species. We also collected ploidy data using chromosome counts and genome size estimates. Bayesian and parsimony trees were congruent with each other and well resolved. Polystachya appears monophyletic based on current sampling, provided that the name P. neobenthamia is used instead of Neobenthamia gracilis for that species. The current sectional classification does not define monophyletic groups, but the present study can be used as the basis for a future sectional classification. Areas postulated as Pleistocene refugia for wet tropical forests in Africa also form centres of diversity for the genus. Biogeographical analyses using DIVA and Lagrange show an early radiation in eastern Africa, followed by separate radiations in eastern and western Africa. Subsequent dispersal from western to eastern Africa has occurred at a much higher rate than from east to west. Dispersal to the Neotropics occurred more than once, and one lineage has spread recently and rapidly throughout the tropics. Polyploidy has occurred several times during the diversification of the genus, most notably in association with the recent pantropical dispersal.

For nearly all species in the three genera of tribe Sinningieae (Gesneriaceae), Sinningia, Paliavana, and Vanhouttea (mostly in southeastern Brazil) plus 10 outgroups, we have sequenced six non-coding DNA regions (i.e., plastid intergenic spacers trnT-trnL, trnL-trnF, trnS-trnG, atpB-rbcL, and introns in the trnL and rpl16 genes) and four introns in nuclear plastid-expressed glutamine synthetase gene (ncpGS). Separate and combined analyses of these data sets using maximum parsimony supported the monophyly of Sinningieae, but the genera Paliavana and Vanhouttea were found embedded within Sinningia; therefore a new infrageneric classification is here proposed. Mapping of pollination syndromes on the DNA-based trees supported multiple origins of hummingbird and bee syndromes and derivation of moth and bat syndromes from hummingbird flowers. Perennial tubers were derived from perennial stems in non-tuberous plants.